Releases: Taiji-pipeline/Taiji
Taiji v1.3.0
Changes in this Release:
- First official release of the single-cell ATAC-seq pipeline.
- A lot of improvements to the single-cell analysis pipeline.
- Create signal enrichment bigwig files for the ATAC-seq pipeline.
- Bugfix: #19
Taiji v1.2.1.3
Changes in this Release:
Taiji v1.2.1
Changes in this Release:
-
Much faster data downloading from GEO by using
fasterq-dumpwhen available. -
Change peak merging algorithm in single cell ATAC-seq analysis.
-
Add
bwa_seed_lengthto the configuration. -
Fix worker pool exhaustion when processes being killed unexpectedly.
-
bug fix: #5
Taiji v1.2.0
Breaking changes:
- Need to include the index prefix when specifying the location of the BWA or RSEM index in config.yml. For example:
(old) path-to-index/bwa_index => (new) path-to-index/bwa_index/GRCh38.fa.
Other changes:
-
Add the option to input "Filtered" Bam files in ATAC-seq.
-
The Taiji is now shipped with C igraph library (no need to install it separately).
-
Add basic input validations.
-
Implement the chromVAR algorithm in single cell ATAC analysis.
-
Bug fixes.
v1.1.0
-
Auto-detect effective genome size for MACS2.
-
Compress BAM files generated by BWA.
-
Reduce memory usage in certain steps.
-
Fix the normalization issue in bigwig file generation.
-
Add more features to single cell RNA-seq analysis pipeline.
-
Add more features to single cell ATAC-seq analysis pipeline.
v1.0.1
This release introduces a lot of new functions, performance improvements and bug fixes.
-
Use promoter accessibility to estimate the gene expression when RNA-seq is not available. This greately improves the results.
-
New interface for Parallelism and distributed computing which supports running jobs on PBS or slurm. The number of jobs and resource usage of each step can now be configured.
-
Add more QCs and visualization, including fragment size distribution, TSS enrichment, signal correlation and so on.
-
Preliminary support for single cell RNA and ATAC analysis.